Bacillus oshimensis sp. nov., a moderately halophilic, non-motile alkaliphile

Alkalicoccobacillus porphyridii sp. nov., isolated from a marine red alga, reclassification of Shouchella plakortidis and Shouchella gibsonii as Alkalicoccobacillus plakortidis comb. nov. and Alkalicoccobacillus gibsonii comb. nov., and emended description of the genus Alkalicoccobacillus Joshi et al. 2022

A Gram-stain-positive alkali-tolerant and strictly aerobic bacterium, designated strain P16T, was isolated from a marine red alga, Porphyridium cruentum, in the Yellow Sea, Republic of Korea. Cells were motile rods with peritrichous flagella and exhibited catalase and oxidase activities. The optimal growth of strain P16T was observed to occur at 30 °C and pH 8.0 and in the presence of 2.0 % (w/v) NaCl. Menaquinone-7 was identified as the sole respiratory quinone. Strain P16T contained anteiso-C15 : 0, iso-C15 : 0, iso-C14 : 0 and iso-C16 : 0, and diphosphatidylglycerol, phosphatidylglycerol and phosphatidylethanolamine as major cellular fatty acids and polar lipids, respectively. The G+C content of strain P16T was 40.8 mol%. Strain P16T was most closely related to Shouchella plakortidis P203T, Shouchella gibsonii DSM 8722T and Alkalicoccobacillus murimartini LMG 21005T with 98.1, 98.1 and 98.0 % 16S rRNA gene sequence similarities, respectively. Phylogenetic analyses based on 16S rRNA gene and genome sequences revealed that strain P16T, S, plakortidis, S. gibsonii and A. murimartini formed a single phylogenetic lineage cluster, and genomic relatedness analyses showed that they are different species. Based on phylogenetic, phenotypic, chemotaxonomic and molecular features, strain P16T represents a novel species of the genus Alkalicoccobacillus, for which the name Alkalicoccobacillus porphyridii sp. nov. is proposed. The type strain is P16T (=KACC 19520T=JCM 32931T). In addition, S. plakortidis and S. gibsonii are reclassified as Alkalicoccobacillus plakortidis comb. nov. (type strain P203T=DSM 19153T=NCIMB 14288T) and Alkalicoccobacillus gibsonii comb. nov. (type strain PN-109T=ATCC 700164T=DSM 8722T=KCCM 41407T), respectively.

Alkalihalobacterium elongatum gen. nov. sp. nov.: An Antibiotic-Producing Bacterium Isolated From Lonar Lake and Reclassification of the Genus Alkalihalobacillus Into Seven Novel Genera

A Gram-stain positive, long, rod-shaped, motile, and spore-forming bacterium (MEB199^T) was isolated from a sediment sample collected from Lonar Lake, India. The strain was oxidase and catalase positive. The strain grew optimally at pH 10, NaCl concentration of 3.5% at 37°C. The major fatty acids were iso-C_15:0, iso-C_16:0, anteiso-C_15:0, and iso-C_17:0. The peptidoglycan contained meso-diaminopimelic acid (meso-DAP). Phosphatidylethanolamine, diphosphatidylglycerol, and phosphatidylglycerol were the major polar lipids of MEB199^T. Phylogenetic analysis based on 16S rRNA gene sequence showed that strain MEB199^T belonged to the family Bacillaceae and exhibited a distinctive position among the members of the genus Alkalihalobacillus (Ahb.). Strain MEB199^T shared the highest 16S rRNA gene sequence similarity with Alkalihalobacillus alkalinitrilicus ANL-iso4^T (98.36%), whereas with type species Ahb. alcalophilus DSM 485^T, it is 94.91%, indicating that strain MEB199^T is distinctly related to the genus Alkalihalobacillus. The G + C content of genomic DNA was 36.47 mol%. The digital DNA-DNA hybridization (dDDH) (23.6%) and average nucleotide identity (ANI) (81%) values between strain MEB199^T and Ahb. alkalinitrilicus ANL-iso4^T confirmed the novelty of this new species. The pairwise identity based on the 16S rRNA gene sequence between the species of genus Alkalihalobacillus ranges from 87.4 to 99.81% indicating the heterogeneity in the genus. The different phylogenetic analysis based on the genome showed that the members of the genus Alkalihalobacillus separated into eight distinct clades. The intra-clade average amino acid identity (AAI) and percentage of conserved proteins (POCP) range from 52 to 68% and 37 to 59%, respectively, which are interspersed on the intra-genera cutoff values; therefore, we reassess the taxonomy of genus Alkalihalobacillus. The phenotypic analysis also corroborated the differentiation between these clades. Based on the phylogenetic analysis, genomic indices, and phenotypic traits, we propose the reclassification of the genus Alkalihalobacillus into seven new genera for which the names Alkalihalobacterium gen. nov., Halalkalibacterium gen. nov., Halalkalibacter gen. nov., Shouchella gen. nov., Pseudalkalibacillus gen. nov., Alkalicoccobacillus gen. nov., and Alkalihalophilus gen. nov. are proposed and provide an emended description of Alkalihalobacillus sensu stricto. Also, we propose the Ahb. okuhidensis as a heterotypic synonym of Alkalihalobacillus halodurans. Based on the polyphasic taxonomic analysis, strain MEB199^T represents a novel species of newly proposed genus for which the name Alkalihalobacterium elongatum gen. nov. sp. nov. is proposed. The type strain is MEB199^T (= MCC 2982^T, = JCM 33704^T, = NBRC 114256^T, = CGMCC 1.17254^T).

Genomic insights into the phylogeny of Bacillus strains and elucidation of their secondary metabolic potential

The genus Bacillus constitutes a plethora of species that have medical, environmental, and industrial applications. While genus Bacillus has been the focus of several studies where genomic data have been used to resolve many taxonomic issues, there still exist several ambiguities. Through the use of in-silico genome-based methods, we tried to resolve the taxonomic anomalies of a large set of Bacillus genomes (n = 178). We also proposed species names for uncharacterized strains and reported genome sequence of a novel isolate Bacillus sp. RL. In the hierarchical clustering on genome-to-genome distances, we observed 11 distinct monophyletic clusters and investigated the functional pathways annotated as the property of these clusters and core-gene content of the entire dataset. Thus, we were able to assert the possible outlier strains (n = 17) for this genus. Analyses of secondary metabolite potential of each strain helped us unravel still unexplored diversity for various biosynthetic genes.

Bacillus miscanthi sp. nov., a alkaliphilic bacterium from the rhizosphere of Miscanthus sacchariflorus

A novel bacterial strain, designated AK13^T (=KACC 21401^T=DSM 109981^T), was isolated from the rhizosphere of Miscanthus sacchariflorus. Strain AK13^T was found to be an aerobic, Gram-stain-positive, endospore-forming and rod-shaped bacterium. It formed yellow circular colonies with smooth convex surfaces. The genomic DNA G+C content of strain AK13^T was estimated to be 40 mol%. Phylogenetic analysis based on 16S rRNA gene sequence similarity showed that this strain was most closely related to Bacillus lehensis MLB2^T (99.4 %), Bacillus oshimensis K11^T (98.8 %) and Bacillus patagoniensis PAT 05^T (96.6 %). The average nucleotide identity values between strain AK13^T and B. lehensis MLB2^T, B. oshimensis K11^T and B. patagoniensis PAT 05^T were 90.93, 91.05 and 71.87 %, respectively, with the digital DNA-DNA hybridization values of 42.7, 42.6 and 18.8 %, respectively. Cells grew at 5-40 °C (optimum, 28-35 °C), pH 6.5-13 (optimum, pH 8-9) and in the presence of 0-13.0 % (w/v) NaCl (optimum, 1 %). The cell wall of strain AK13^T contained meso-diaminopimelic acid, and the major isoprenoid quinone was MK-7. Results of fatty acid methyl ester analysis revealed that iso-C_{15 : 0} was the predominant cellular fatty acid. Two-dimensional thin-layer chromatography analysis indicated that the major polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine and glycolipid. The genotypic and phenotypic characteristics suggested that strain AK13^T represented a novel species of the genus Bacillus, and thus the name Bacillus miscanthi sp. nov. is proposed.

A phylogenomic and comparative genomic framework for resolving the polyphyly of the genus Bacillus: Proposal for six new genera of Bacillus species, Peribacillus gen. nov., Cytobacillus gen. nov., Mesobacillus gen. nov., Neobacillus gen. nov., Metabacillus gen. nov. and Alkalihalobacillus gen. nov

The genus Bacillus, harbouring 293 species/subspecies, constitutes a phylogenetically incoherent group. In the absence of reliable means for grouping known Bacillus species into distinct clades, restricting the placement of new species into this genus has proven difficult. To clarify the evolutionary relationships among Bacillus species, 352 available genome sequences from the family Bacillaceae were used to perform comprehensive phylogenomic and comparative genomic analyses. Four phylogenetic trees were reconstructed based on multiple datasets of proteins including 1172 core Bacillaceae proteins, 87 proteins conserved within the phylum Firmicutes, GyrA-GyrB-RpoB-RpoC proteins, and UvrD-PolA proteins. All trees exhibited nearly identical branching of Bacillus species and consistently displayed six novel monophyletic clades encompassing 5-23 Bacillus species (denoted as the Simplex, Firmus, Jeotgali, Niacini, Fastidiosus and Alcalophilus clades), interspersed with other Bacillaceae species. Species from these clades also generally grouped together in 16S rRNA gene trees. In parallel, our comparative genomic analyses of Bacillus species led to the identification of 36 molecular markers comprising conserved signature indels in protein sequences that are specifically shared by the species from these six observed clades, thus reliably demarcating these clades based on multiple molecular synapomorphies. Based on the strong evidence from multiple lines of investigations supporting the existence of these six distinct 'Bacillus' clades, we propose the transfer of species from these clades into six novel Bacillaceae genera viz. Peribacillus gen. nov., Cytobacillus gen. nov., Mesobacillus gen. nov., Neobacillus gen. nov., Metabacillus gen. nov. and Alkalihalobacillus gen. nov. These results represent an important step towards clarifying the phylogeny/taxonomy of the genus Bacillus.

Salar del Hombre Muerto, source of lithium-tolerant bacteria

The Salar del Hombre Muerto is a flat salt with great microbial activity despite the existing extreme conditions like high altitude, lack of water, low level of oxygen, high radiation and high concentration of sodium and lithium chloride. Despite these unfavorable conditions, we found microbial diversity with the presence of fungi, algae, and bacteria. From aqueous solutions and soil samples, a total of 238 bacteria were isolated and 186 of them were able to grow in the presence of salt. About 30% of the strains showed the ability to grow in solid medium proximally to a LiCl solution close to saturation (636 g/L). These isolates were characterized taking into account the morphology, Gram stain, ability to form biofilms and to produce pigments, and mainly according to the tolerance against lithium chloride. Bacillus was predominant among the most tolerant 26 microorganisms found, followed by Micrococcus and Brevibacterium. Members of the genera Kocuria, Curtobacterium and Halomonas were also represented among the bacteria with tolerance to 30 and 60 g/L of LiCl in defined liquid medium. All the capacities found in these microorganisms make them extremely interesting for biotechnological applications.

Taxonomic description and genome sequence of Bacillus campisalis sp. nov., a member of the genus Bacillus isolated from a solar saltern

The taxonomic position of a Gram-stain positive bacterium isolated from a solar saltern sample collected from Kanyakumari, coastal region of the Bay of Bengal, India, was analysed by using a polyphasic approach. The isolated strain, designated SA2-6T, had phenotypic characteristics that matched those of the genus Bacillus. The 16S rRNA gene sequence (1493 bases) of the novel strain was compared with those of previously studied Bacillus type strains and confirmed that the strain belongs to the genus Bacillus and was moderately closely related to the type strain of Bacillus foraminis at 97.5 % 16S rRNA gene sequence similarity, followed by those of Bacillus thioparans (96.9 %), Bacillus subterraneus (96.8 %), Bacillus jeotgali (96.6 %), Bacillus selenatarsenatis (96.6 %) and Bacillus boroniphilus (96.6 %). 16S rRNA gene sequence analysis indicated that strain SA2-6T differs from all other species of the genus Bacillus by at least 2.5 %. It contained MK-7 as the predominant menaquinone, meso-diaminopimelic acid as the diagnostic cell-wall diamino acid, and iso-C15 : 0 and anteiso-C15 : 0 as major fatty acids. Major lipids were diphosphatidylglycerol (DPG), phosphatidylglycerol (PG) and phosphatidylethanolamine (PE). Based on data from this polyphasic study, strain SA2-6T is considered to represent a novel species of the genus Bacillus, for which the name Bacillus campisalis sp. nov. is proposed. The type strain is SA2-6T ( = MTCC 11848T = DSM 28801T). The draft genome of strain SA2-6T consisted of 5 183 363 bp with G+C content of 45.44 mol%, 5352 predicted coding sequences, 191 RNAs and 479 subsystems.

Bacterial treatment of alkaline cement kiln dust using Bacillus halodurans strain KG1

This study was conducted to isolate an acid-producing, alkaliphilic bacterium to reduce the alkalinity of cement industry waste (cement kiln dust). Gram-positive isolate KG1 grew well at pH values of 6–12, temperatures of 28–50 °C, and NaCl concentrations of 0–16% and thus was further screened for its potential to reduce the pH of an alkaline medium. Phenotypic characteristics of the KG1 isolate were consistent with those of the genus Bacillus, and the highest level of 16S rRNA gene sequence similarity was found with Bacillus halodurans strain DSM 497 (94.7%). On the basis of its phenotypic characteristics and genotypic distinctiveness from other phylogenetic neighbors belonging to alkaliphilic Bacillus species, the isolated strain was designated B. halodurans strain KG1, with GenBank accession number JQ307184 (= NCIM 5439). Isolate KG1 reduced the alkalinity (by 83.64%) and the chloride content (by 86.96%) of cement kiln dust and showed a potential to be used in the cement industry for a variety of applications.

Rhizobium pakistanensis sp. nov., isolated from groundnut (Arachis hypogaea) nodules grown in rainfed Pothwar, Pakistan

A Gram-negative, white, non-motile, rod shaped bacterial strain BN-19(T) was isolated from a root nodule of groundnut (Arachis hypogaea) in Pakistan. Phylogenetic analysis based on 16S rRNA gene sequence revealed that strain BN-19(T) formed a subclade in the genus Rhizobium together with Rhizobium alkalisoli CCBAU 01393(T), Rhizobium vignae CCBAU 05176(T), Rhizobium huautlense SO2(T) and Rhizobium tarimense PL-41(T) with sequence similarities of 97.5, 97.3, 97.2 and 97.1 % respectively. Sequence analysis of housekeeping genes atpD, glnII and recA (with sequence similarities of ≤92 %) confirmed the unique position of BN-19(T) in the genus Rhizobium. DNA-DNA relatedness between the strain BN-19(T) and R. alkalisoli CCBAU 01393(T), R. vignae CCBAU 05176(T), R. huautlense SO2(T) and R. tarimense PL-41(T) were 20.6, 22.5, 15.9 and 20.5 % respectively, further confirming that BN-19(T) represents a novel species in the genus Rhizobium. The DNA G + C content was 60.1 mol%. The dominant fatty acids of strain BN-19(T) were C19:0 cyclo ω8c, summed feature 2 (C14:0 3OH and/or C16:1 iso I) and summed feature 8 (C18:1 ω7c). Some phenotypic features also differentiate the strain BN-19(T) from the related species. On the basis of these results, strain BN-19(T) is considered to represent a novel species in the genus Rhizobium, for which the name Rhizobium pakistanensis sp. nov. is proposed. The type strain is BN-19(T) (=LMG 27895(T) = CCBAU 101086(T)).

Evolution in the Bacillaceae

The family Bacillaceae constitutes a phenotypically diverse and globally ubiquitous assemblage of bacteria. Investigation into how evolution has shaped, and continues to shape, this family has relied on several widely ranging approaches from classical taxonomy, ecological field studies, and evolution in soil microcosms to genomic-scale phylogenetics, laboratory, and directed evolution experiments. One unifying characteristic of the Bacillaceae , the endospore, poses unique challenges to answering questions regarding both the calculation of evolutionary rates and claims of extreme longevity in ancient environmental samples.

Bacillus xiaoxiensis sp. nov., a slightly halophilic bacterium isolated from non-saline forest soil

A novel Gram-stain-positive, slightly halophilic, catalase-positive, oxidase-negative, endospore-forming, motile, facultatively anaerobic, rod-shaped bacterium, designated strain JSM 081004T, was isolated from non-saline forest soil in Xiaoxi National Natural Reserve, China. Growth occurred with 0.5–20 % (w/v) NaCl (optimum 2–4 %), at pH 6.0–10.5 (optimum pH 8.0) and at 5–40 °C (optimum 25–30 °C). meso-Diaminopimelic acid was present in the cell-wall peptidoglycan. The major cellular fatty acids were iso-C15 : 0 and anteiso-C15 : 0. Strain JSM 081004T contained MK-7 as the predominant respiratory quinone, and diphosphatidylglycerol, phosphatidylethanolamine and phosphatidylglycerol as the major polar lipids. The genomic DNA G+C content of strain JSM 081004T was 40.1 mol%. Phylogenetic analysis based on 16S rRNA gene sequence comparisons revealed that strain JSM 081004T should be assigned to the genus Bacillus and was most closely related to the type strains of Bacillus lehensis (sequence similarity 97.8 %), Bacillus oshimensis (97.8 %) and Bacillus patagoniensis (97.3 %). Phylogenetic analysis, DNA–DNA relatedness values, phenotypic characteristics and chemotaxonomic data all support the proposal of strain JSM 081004T as a representative of a novel species of the genus Bacillus, for which the name Bacillus xiaoxiensis sp. nov. is proposed; the type strain is JSM 081004T ( = CCTCC AA 208057T  = DSM 21943T).

Bacillus alkalisediminis sp. nov., an alkaliphilic and moderately halophilic bacterium isolated from sediment of extremely shallow soda ponds

Alkaliphilic strains characterized by optimal growth at pH 9.0 and 5 % (w/v) NaCl designated K1-25T and H3-93 were isolated from extremely shallow soda ponds located in Hungary. Cells of both strains were Gram-stain-positive, non-motile, straight rods and formed central, ellipsoidal endospores with swollen sporangia. The isolates were aerobic, catalase-positive, oxidase-negative and contained a peptidoglycan of type A1γ based on meso-diaminopimelic acid. In both strains, menaquinone-7 (MK-7) was the predominant isoprenoid quinone and the major cellular fatty acids were anteiso-C15 : 0 and iso-C15 : 0. The DNA G+C contents of strains K1-25T and H3-93 were 39.0 and 36.3 mol%, respectively. 16S rRNA gene sequence-based phylogenetic analysis revealed 99.2 % similarity between strains K1-25T and H3-93 and the novel isolates had the highest similarities to Bacillus akibai 1139T (97.8 and 98.3 %, respectively), Bacillus wakoensis N-1T (97.0 and 97.4 %), Bacillus okhensis Kh10-101T (97.1 and 97.4 %) and Bacillus krulwichiae AM31DT (96.9 and 97.1 %). DNA–DNA hybridization between our strains and the type strains of closely related Bacillus species was lower than 70 %. Although DNA–DNA hybridization between strains K1-25T and H3-93 was 27 %, the phenotypic and chemotaxonomic data did not support the differentiation of these two strains into separate species. Therefore, they represent genomovars of a novel species, for which the name Bacillus alkalisediminis sp. nov. is proposed. The type strain is K1-25T ( = DSM 21670T  = NCAIM B02301T).

Bacillus hunanensis sp. nov., a slightly halophilic bacterium isolated from non-saline forest soil

A novel Gram-stain-positive, slightly halophilic, catalase- and oxidase-positive, endospore-forming, motile, aerobic, rod-shaped bacterium, designated strain JSM 081003(T), was isolated from non-saline forest soil in Hunan Province, China. Growth occurred with 0.5-15% (w/v) NaCl (optimum 2-4%) at pH 6.5-10.5 (optimum pH 7.5-8.5) and at 5-40 °C (optimum 30 °C). meso-Diaminopimelic acid was present in the cell-wall peptidoglycan. The major cellular fatty acids were iso-C15:0, anteiso-C15:0 and iso-C14:0. Strain JSM 081003(T) contained MK-7 as the predominant respiratory quinone, and diphosphatidylglycerol, phosphatidylethanolamine and phosphatidylglycerol as the major polar lipids. The genomic DNA G + C content of strain JSM 081003(T) was 40.9 mol%. A phylogenetic analysis based on 16S rRNA gene sequence comparisons revealed that strain JSM 081003(T) should be assigned to the genus Bacillus, and was related most closely to the type strains of Bacillus lehensis (sequence similarity 99.6%), Bacillus oshimensis (99.4%) and Bacillus patagoniensis (96.6%); lower than 96.0% sequence similarity was observed with other Bacillus species. The combination of phylogenetic analysis, DNA-DNA relatedness values, phenotypic characteristics and chemotaxonomic data supports the view that strain JSM 081003(T) represents a new species of the genus Bacillus, for which the name Bacillus hunanensis sp. nov. is proposed. The type strain is JSM 081003(T) (= DSM 23008(T) = KCTC 13711(T)).

Bacillus trypoxylicola sp. nov., xylanase-producing alkaliphilic bacteria isolated from the guts of Japanese horned beetle larvae (Trypoxylus dichotomus septentrionalis)

Three xylanase-producing alkaliphilic strains, SU1T, 36AC4 and 36AC6, were isolated from the guts of larvae of the Japanese horned beetle (Trypoxylus dichotomus septentrionalis). The isolates stained Gram-positive and were aerobic, spore-forming, non-motile and rod-shaped and grew optimally at 30 °C and pH 9. They contained MK-7 as the major isoprenoid quinone and iso-C15 : 0, anteiso-C15 : 0, anteiso-C17 : 0 and iso-C17 : 0 as the major fatty acids. The DNA G+C contents of the strains were 37.4–37.7 mol%. On the basis of 16S rRNA gene sequence similarity, these strains were shown to belong to the genus Bacillus. Although their 16S rRNA gene sequence similarity to the type strains of the alkaliphilic species Bacillus pseudalcaliphilus and B. alcalophilus was 97 %, the novel isolates formed a distinct group in the phylogenetic trees and DNA–DNA relatedness values to the type strains of these species were less than 30 %. Results of physiological and biochemical tests, including salt preference, enabled these strains to be differentiated phenotypically from described Bacillus species. Therefore, strains SU1T, 36AC4 and 36AC6 represent a novel species for which the name Bacillus trypoxylicola sp. nov. is proposed; the type strain is SU1T (=NBRC 102646T =KCTC 13244T).

Geomicrobium halophilum gen. nov., sp. nov., a moderately halophilic and alkaliphilic bacterium isolated from soil

Two moderately halophilic and alkaliphilic bacteria, designated strains BH1(T) and HN5, were isolated from forest soil and garden soil, respectively, in Japan. Cells of strains BH1(T) and HN5 were non-motile, aerobic, bean-shaped, formed irregular clusters with 2-20 cells, Gram-positive and contained A1gamma, meso-diaminopimelic acid-type murein. Spore formation was not detected. Growth occurred in 5-25 % (w/v) NaCl (optimum, 10-15 %, w/v), at pH 6.0-10.0 (optimum, pH 8.5-9.0) and at 20-40 degrees C (optimum, 30 degrees C). The predominant isoprenoid quinones were menaquinone-7 and menaquinone-6. The phospholipids were diphosphatidylglycerol and phosphatidylglycerol. The major cellular fatty acids were i-C(15 : 0), i-C(17 : 0) and i-C(18 : 0). The DNA G+C content of strains BH1(T) and HN5 was 45 and 46 mol%, respectively. The 16S rRNA gene sequences of the two strains were 99.9 % similar. DNA-DNA hybridization results indicated high levels of relatedness (88 and 85 % reciprocally). Similarities with recognized species were less than 90.2 %. The phylogenetic and phenotypic characteristics indicated that strains BH1(T) and HN5 represent a novel species in a new genus, for which the name Geomicrobium halophilum gen. nov., sp. nov. is proposed. The type strain is BH1(T) (=JCM 15647(T)=DSM 21769(T)).

An organic-solvent-tolerant esterase from thermophilic Bacillus licheniformis S-86

A thermophile, halotolerant and organic-solvent-tolerant esterase producer Bacillus sp. S-86 strain previously isolated was found to belong to Bacillus licheniformis species through morphological, biochemical, 16S rRNA gene sequence analyses and rDNA intergenic spacers amplification (ITS-PCR). The strain can grow at 55 degrees C in presence of C2-C7 alkanols (log P=-0.86 to 2.39), and NaCl concentrations up to 15% (w/v). This bacterium showed optimal growth and esterase production at 50 degrees C. Two different molecular weight esterase activities were detected in zymographic assays. PMSF inhibited type I esterase activity, showing no inhibitory effect on type II esterase activity. B. licheniformis S-86 was able to grow in presence of hydroxylic organic-solvents like propan-2-ol, butan-1-ol and 3-methylbutan-1-ol. At a sub-lethal concentration of these solvents (392 mmoll(-1) propan-2-ol; 99 mmol l(-1) butan-1-ol, 37 mmol l(-1) 3-methylbutan-1-ol), adequate to produce 50% cell growth inhibition at 50 degrees C, an increment between 1.9 and 2.3 times was observed in type I esterase production, and between 2.2 and 3.1 times in type II esterase production.

Alkalibacillus silvisoli sp. nov., an alkaliphilic moderate halophile isolated from non-saline forest soil in Japan

Two alkaliphilic, moderately halophilic bacteria, designated BM2(T) and HN2, were isolated from non-saline forest soil in Japan. The cells of strain BM2(T) were motile, aerobic, rod-shaped and Gram-positive. The peptidoglycan was of the A1gamma type, and the diamino acid was meso-diaminopimelic acid. Growth was observed at NaCl concentrations between 5.0 and 25.0 % (w/v) (the optimum being 10.0-15.0 %, w/v), at pH 7.0-10.0 (optimum, pH 9.0-9.5) and at 20-50 degrees C. The predominant isoprenoid quinone was MK-7. The major cellular fatty acids were iso-C(15 : 0) and anteiso-C(17 : 0). The G+C content of total DNA of strain BM2(T) was 37.0 mol%. Phylogenetic analysis of the 16S rRNA gene sequence showed that strain BM2(T) was most closely related to Alkalibacillus haloalkaliphilus DSM 5271(T) (98.0 % sequence similarity). DNA-DNA hybridization results indicated low levels of relatedness between strain BM2(T) and A. haloalkaliphilus JCM 12303(T) (23 and 16 % reciprocally), Alkalibacillus filiformis JCM 13893(T) (25 and 21 %) and Alkalibacillus salilacus JCM 13894(T) (27 and 19 %). On the basis of the phylogenetic and phenotypic characteristics, strain BM2(T) represents a novel species, for which the name Alkalibacillus silvisoli sp. nov. is proposed. The type strain is BM2(T) (=JCM 14193(T)=DSM 18495(T)).

Bacillus lehensis sp. nov., an alkalitolerant bacterium isolated from soil

A Gram-positive, endospore-forming, alkalitolerant bacterial strain, designated MLB2T, was isolated from soil from Leh, India, and was subjected to a polyphasic taxonomic study. The strain exhibited phenotypic properties that included chemotaxonomic characteristics consistent with its classification in the genusBacillus. Growth was observed at pH 7.0–11.0, but not at pH 6.0. The DNA G+C content was 41.4 mol%. The highest level of 16S rRNA gene sequence similarity was withBacillus oshimensisJCM 12663T(98.8 %). However, DNA–DNA hybridization experiments indicated low levels of genomic relatedness with the type strains ofB. oshimensis(62 %),Bacillus patagoniensis(55 %),Bacillus clausii(51 %) andBacillus gibsonii(34 %), the species with which strain MLB2Tformed a coherent cluster (based on the results of the phylogenetic analysis). On the basis of the phenotypic characteristics and genotypic distinctiveness of strain MLB2T, it should be classified within a novel species ofBacillus, for which the nameBacillus lehensissp. nov. is proposed. The type strain is MLB2T(=MTCC 7633T=JCM 13820T).

Bacteroides finegoldii sp. nov., isolated from human faeces

Two strains, 199T and 176, of Gram-negative, anaerobic, rod-shaped, non-spore-forming bacteria were isolated during studies of microbiota in human faeces using polyamine-deficient medium. Phylogenetic analysis based on 16S rRNA gene sequences revealed that the isolated strains belonged to the genus Bacteroides. The G+C content (42.4-43.0 mol%) and major fatty acid composition (anteiso-C15:0, 31.8-36.2 %) supported the affiliation of the two strains to the genus Bacteroides. 16S rRNA gene sequence similarities with their closest neighbours, Bacteroides thetaiotaomicron and Bacteroides ovatus, ranged from 94.6 to 96.5 %. DNA-DNA hybridization and phenotypic analysis showed that the two strains belonged to the same species (DNA-DNA relatedness of 89 %) and were distinct from their close relatives, B. thetaiotaomicron and B. ovatus (<23 % DNA-DNA relatedness). On the basis of these data, a novel species of the genus Bacteroides, Bacteroides finegoldii sp. nov., is proposed, comprising the designated type strain 199T (=JCM 13345T=DSM 17565T) and strain 176 (=JCM 13346).

Cytochrome c and bioenergetic hypothetical model for alkaliphilic Bacillus spp

Although a bioenergetic parameter is unfavorable for production of ATP (DeltapH<0), the growth rate and yield of alkaliphilic Bacillus strains are higher than those of neutralophilic Bacillus subtilis. This finding suggests that alkaliphiles possess a unique energy-producing machinery taking advantage of the alkaline environment. Expected bioenergetic parameters for the production of ATP (DeltapH and DeltaPsi) do not reflect the actual parameters for energy production. Certain strains of alkaliphilic Bacillus spp. possess large amounts of cytochrome c when grown at a high pH. The growth rate and yield are higher at pH 10 than at pH 7 in facultative alkaliphiles. These findings suggest that a large amount of cytochrome c at high pHs (e.g., pH 10) may be advantageous for sustaining growth. To date, isolated cytochromes c of alkaliphiles have a very low midpoint redox potential (less than +100 mV) compared with those of neutralophiles (approximately +220 mV). On the other hand, the redox potential of the electron acceptor from cytochrome c, that is, cytochrome c oxidase, seems to be normal (redox potential of cytochrome a=+250 mV). This large difference in midpoint redox potential between cytochrome c and cytochrome a concomitant with the configuration (e.g., a larger negative ion capacity at the inner surface membrane than at the outer surface for the attraction of H+ to the intracellular membrane and a large amount of cyrochrome c) supporting H+-coupled electron transfer of cytochrome c may have an important meaning in the adaptation of alkaliphiles at high pHs. This respiratory system includes a more rapid and efficient H+ and e- flow across the membrane in alkaliphiles than in neutralophiles.

Characterization of alkaliphilic Bacillus strains used in industry: proposal of five novel species

Twenty alkaliphilic bacterial strains from industrial applications or enzyme studies were subjected to a polyphasic taxonomic investigation, including 16S rRNA gene sequencing, determination of genomic DNA G+C content, DNA–DNA hybridization, fatty acid analysis and standard bacteriological characterization. By comparing the groupings obtained based on the genomic DNA G+C content and the construction of a phylogenetic tree based on the 16S rRNA gene sequence, 12 clusters of similar strains were recognized. DNA–DNA hybridization revealed that these clusters represented five novel genospecies. Further analysis supported the proposal of five novel species in the genus Bacillus: Bacillus wakoensis sp. nov. (type strain N-1T=JCM 9140T=DSM 2521T), Bacillus hemicellulosilyticus sp. nov. (type strain C-11T=JCM 9152T=DSM 16731T), Bacillus cellulosilyticus sp. nov. (type strain N-4T=JCM 9156T=DSM 2522T), Bacillus akibai sp. nov. (type strain 1139T=JCM 9157T=ATCC 43226T) and Bacillus mannanilyticus sp. nov. (type strain AM-001T=JCM 10596T=DSM 16130T).

Alkalibacillus filiformis sp. nov., isolated from a mineral pool in Campania, Italy

A halo-alkaliphilic, Gram-positive, non-motile bacterium, designated strain 4AGT, was isolated from a mineral pool located in Malvizza, Campania, southern Italy. On the basis of 16S rRNA gene sequence analysis, strain 4AGT was shown to belong to the genus Alkalibacillus within the phylum Firmicutes; its phylogenetic distance from recognized Alkalibacillus species was <95·0 %. Chemotaxonomic data (MK-7 as the major menaquinone; directly cross-linked meso-diaminopimelic acid in the cell wall; phosphatidylglycerol and diphosphatidylglycerol as major polar lipids; iso-C15 : 0, anteiso-C15 : 0 and iso-C17 : 0 as major fatty acids; and glycine betaine and glutamate as major compatible solutes) supported the affiliation of the strain to the genus Alkalibacillus. The results of DNA–DNA hybridization and physiological and biochemical tests allowed genotypic and phenotypic differentiation of strain 4AGT from the two recognized Alkalibacillus species. Strain 4AGT therefore represents a novel species, for which the name Alkalibacillus filiformis sp. nov. is proposed. The type strain is 4AGT (=DSM 15448T=ATCC BAA-956T).